Mass spectrometry is a powerful tool for the identification of proteins and the determination of their structures and properties. The scientific community routinely employs MS-based proteomics. A new opportunity, protein footprinting, is emerging that takes advantage of these refined proteomics capabilities that combine high performance liquid chromatography and mass spectrometry. The development of these techniques is driven by a growing number of collaborative projects in biomedical science and other fields. The Washington University Mass Spectrometry Resource (WUMSR) has played a key role in the development of protein footprinting for more than a decade and is an ideal place to support its expansion. While it does not yet have the resolution of X-ray crystallography and NMR, MS-based footprinting is significantly more specific than the low resolution tools of CD, fluorescence, Raman, absorbance, SPR, and calorimetry. In addition footprinting occurs while the proteins and their complexes are in their native states, affording relevant measurements of many important thermodynamic and kinetic parameters. Footprinting approaches include hydrogen deuterium exchange (H/DX), fast photochemical oxidation of proteins (FPOP), and other amino acid specific chemical modifications. To fulfill and disseminate the promise of protein footprinting, we propose to add a high performance, LC/MS system and commit it full time to support this research. The proposed instrument will be used to address the needs of 17 collaborators who have problems in protein biochemistry and medicine. The proteins have implications in cancer, viral infections, pain management, and brain disorders, principally Alzheimer's disease (AD). There are implications as well as in energy and photosynthesis. The approaches will enable studies of protein folding and unfolding, permit the determination of interfaces between important peptides (e.g., A? with implications in AD), determine binding interfaces of small ligands including potential drugs, and measure the affinities of binding. We will extend these measurements to protein assemblies, including those that are membrane-bound. Given that the footprinting experiments produce data that constrains protein and protein-complex structure, just as in NMR, we predict that we can ultimately use these data to obtain coarse-grained structures, even in the absence of high resolution structural data. Progress in this area will impact a broad range of protein science with consequent effects on improving human health.